gphys 1.5.5 → 1.5.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/ChangeLog

@@ -1,3 +1,80 @@
+2019-03-19  Takeshi Horinouchi
+To release version 1.5.6 (git tag v1.5.6)
+
+M	lib/numru/gphys/version.rb
+
+2019-03-19  Takeshi Horinouchi
+Update the years (to -2019)
+
+M	LICENSE.txt
+
+2019-03-19  Takeshi Horinouchi
+to require 'numru/gphys/derivative' from the begining
+
+M	lib/numru/gphys.rb
+
+2019-02-28  Takeshi Horinouchi
+Fitting::least_square_fit: bug fix of best fit when with_offset==false
+
+M	lib/numru/ganalysis/fitting.rb
+
+2019-01-13  Takeshi Horinouchi
+GAnalysis::PDE::SOR_2D_2ndorder : added an option "ignore_non_eliptic". Changed optional arguments to keyword arguments.
+
+M	ext/numru/ganalysis/pde_ext.c
+M	lib/numru/ganalysis/pde.rb
+
+2018-12-09  Takeshi Horinouchi
+bug fix
+
+M	lib/numru/ganalysis/narray_ext.rb
+
+2018-12-09  Takeshi Horinouchi
+Update and bug fix
+
+M	ext/numru/ganalysis/pde_ext.c
+M	lib/numru/ganalysis/pde.rb
+
+2018-12-06  Takeshi Horinouchi
+Created NArray#cum_sum which accepts multi-D NArray unlike NArray#cumsum
+
+M	ext/numru/ganalysis/ext_init.c
+A	ext/numru/ganalysis/narray_ext_dfloat.c
+A	lib/numru/ganalysis/narray_ext.rb
+
+2018-12-04  Takeshi Horinouchi
+Added ext/numru/ganalysis/extconf.rb
+
+M	gphys.gemspec
+
+2018-12-04  Takeshi Horinouchi
+Created GAnalysis::PDE and its method SOR_2D_2ndorder (to solve 2D 2nd order PDE by SOR)
+
+A	ext/numru/ganalysis/ext_init.c
+A	ext/numru/ganalysis/extconf.rb
+A	ext/numru/ganalysis/pde_ext.c
+A	lib/numru/ganalysis/pde.rb
+
+2018-11-29  Takeshi Horinouchi
+least_square_fit: added an option with_offset
+
+M	lib/numru/ganalysis/fitting.rb
+
+2018-11-29  Takeshi Horinouchi
+tone: Improved treatment of fullcolor
+
+M	lib/numru/ggraph.rb
+
+2018-11-29  Takeshi Horinouchi
+Added no_sort option to join_md.
+
+M	lib/numru/gphys/gphys.rb
+
+2018-04-09  Takeshi Horinouchi
+completed the change in b86d44ca18fca98bb
+
+M	lib/numru/ganalysis/eof.rb
+
 2018-03-20  Takeshi Horinouchi
 To release version 1.5.5 (git tag v1.5.5)
 

data/LICENSE.txt

@@ -1,7 +1,7 @@
 GPhys is copyrighted free software by Takeshi Horinouchi and
 GFD Dennou Club (http://www.gfd-dennou.org/).
 
-Copyright 2003-2018 (C) Takeshi Horinouchi and GFD Dennou Club
+Copyright 2003-2019 (C) Takeshi Horinouchi and GFD Dennou Club
 (http://www.gfd-dennou.org/) All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

data/ext/numru/ganalysis/ext_init.c

@@ -0,0 +1,9 @@
+void init_ganalysis_pde_ext();
+void init_narray_ext_dfloat();
+
+void
+Init_ganalysis_ext()
+{
+    init_ganalysis_pde_ext();
+    init_narray_ext_dfloat();
+}

data/ext/numru/ganalysis/extconf.rb

@@ -0,0 +1,43 @@
+require 'mkmf'
+gem_path = nil
+
+if Gem.respond_to?(:find_files) and Gem.find_files("narray.h").length > 0
+  require "rbconfig"
+  so = RbConfig::CONFIG["DLEXT"]
+  narray_include = File.expand_path(File.dirname(Gem.find_files("narray.h")[0]))
+  narray_lib = File.expand_path(File.dirname(Gem.find_files("narray." + so)[0]))
+else
+  gem_home=(`gem environment GEM_HOME`).chomp
+  narray_dir = Dir.glob("#{gem_home}/gems/narray-*/ext/narray").sort[-1]
+  if narray_dir
+    narray_include = narray_lib = narray_dir
+  else
+    narray_include = narray_lib = [ $sitearchdir, $vendorarchdir]
+  end
+end
+dir_config('narray', narray_include, narray_lib)
+
+require "narray"
+if NArray.const_defined?(:SUPPORT_BIGMEM) && NArray::SUPPORT_BIGMEM
+
+  case RbConfig::CONFIG["CC"]
+  when "gcc"
+    omp_opt = "-fopenmp"
+  else
+    omp_opt = nil
+  end
+  omp_opt = arg_config("--openmp", omp_opt)
+
+  omp_opt = nil if omp_opt.to_s.empty?
+
+  if omp_opt
+    $CFLAGS << " " << omp_opt
+    $DLDFLAGS << " " << omp_opt
+    warn "OpenMP support: ON"
+  else
+    warn "OpenMP support: OFF"
+    warn "if you want to enable openmp, set --openmp=compile_option"
+  end
+end
+
+create_makefile('numru/ganalysis_ext')

data/ext/numru/ganalysis/narray_ext_dfloat.c

@@ -0,0 +1,84 @@
+/* narray_ext_dfloat.c : Extention library of NArray (DFLOAT only)
+ */
+#include<stdio.h>
+#include<string.h>
+#include "ruby.h"
+#include "narray.h"
+#ifndef NARRAY_BIGMEM
+typedef int na_shape_t;
+#endif
+
+typedef double c_num_t;
+#define NATYPE NA_DFLOAT
+
+static VALUE
+cum_sum_dfloat(obj, self, dim)
+     VALUE obj;
+     VALUE self;
+     VALUE dim;
+{
+    VALUE res;
+    int d, dj, rank;
+    struct NARRAY *na;
+    na_shape_t i, j, k, ni, nj, nk, nij;
+    na_shape_t *sh;
+    c_num_t *p, *c;
+    
+    /* check & read arguments */
+    dj = NUM2INT(dim);
+
+    if (NA_TYPE(self) != NATYPE) rb_raise(rb_eArgError,"Unexpected type");
+    rank = NA_RANK(self);
+    if (dj<-rank || dj>=rank) rb_raise(rb_eArgError,
+                     "dim (%d) out of range (%d to %d)", dj, -rank, rank-1);
+    if (dj<0) dj += rank;
+    
+    /* interpret shape as 3D */
+    GetNArray(self, na);
+    sh = na->shape;
+    p = (c_num_t *) NA_PTR(na, 0);
+    ni = 1;
+    for(d=0; d<dj; d++) ni *= sh[d];
+    nj = sh[dj];
+    nij = ni*nj;
+    nk = 1;
+    for(d=dj+1; d<rank; d++) nk *= sh[d];
+
+    /* initialize the output object */
+    res = na_make_object(NATYPE, rank, sh, cNArray);
+    GetNArray(res, na);
+    c = (c_num_t *) NA_PTR(na, 0);
+
+    /* operation */
+    for(k=0; k<nk; k++){
+        for(i=0; i<ni; i++){
+            c[i+nij*k] = p[i+nij*k];   /* copy the first element */
+        }
+    }
+    for(k=0; k<nk; k++){
+        for(j=1; j<nj; j++){
+            for(i=0; i<ni; i++){
+                c[i+ni*j+nij*k] = p[i+ni*j+nij*k] + c[i+ni*(j-1)+nij*k];
+            }
+        }
+    }
+
+    return(res);
+}
+
+
+// VALUE cNArray;
+
+void
+init_narray_ext_dfloat()
+{
+    /* 以下はどうもうまく行かない。(NArrayが拡張ライブラリだからか)
+       rb_require("narray");
+       // cNArray = rb_define_class("NArray", rb_cObject);
+       rb_define_method(cNArray, "cum_sum_dfloat", cum_sum_dfloat, 1);
+     */
+    static VALUE mNumRu, mNArrayExt;
+    mNumRu = rb_define_module("NumRu");
+    mNArrayExt = rb_define_module_under(mNumRu, "NArrayExt");
+    rb_define_module_function(mNArrayExt, "cum_sum_dfloat", cum_sum_dfloat, 2);
+}

data/ext/numru/ganalysis/pde_ext.c

@@ -0,0 +1,130 @@
+/* c_pde.c : Extention library for partial differential equation solvers
+ * All in NArray
+ */
+
+#include<stdio.h>
+#include<string.h>
+#include<math.h>
+#include "ruby.h"
+#include "narray.h"
+
+/* for compatibility for NArray and NArray with big memory patch */
+#ifndef NARRAY_BIGMEM
+typedef int na_shape_t;
+#endif
+
+#define ID(i,j) ((i)+nx*(j))
+
+/* Eq: A z_xx + 2 B z_xy + C z_yy + D z_x + E z_y = F
+ *              ^^^
+ *
+ * Assumption: dx and dy are constants (uniform).
+ * Boundary values are not changed. --> change afterwords if not Dirichlet.
+ *
+ * Basic discretization: by central differences:
+ *   A/dx^2 (z[i-1,j]-2z[i,j]+z[i+1,j])
+ *   + B/(2dxdy) ((z[i+1,j+1]-z[i-1,j+1]-z[i+1,j-1]+z[i-1,j-1])
+ *   + C/dy^2 (z[i,j-1]-2z[i,j]+z[i,j+1])
+ *   + D/(2dx) (z[i+1,j]-z[i-1,j]) + E/(2dy) (z[i,j+1]-z[i,j-1]) - F = 0
+ * 
+ * * Z [2D Float(=DFLOAT) NArray] (inout) -- to be overwritten
+ * * A, B, ... [2D Float(=DFLOAT) NArray] coeffitients
+ * * OME [Float] constant, which should 1<= OME < 2 (Gauss-Seidel if OME=1)
+ * * Return value: res = |H dz| (L2 norm),
+ *   where H = 2(diag(A)/dx^2+diag(C)/dy^2).
+ *   Convergence can be judged by res/|F| < eps
+ */
+static VALUE
+SOR_2D_2ndorder_1step(obj, Z, A, B, C, D, E, F, DX, DY, OME, Ignore_non_eliptic)
+     VALUE obj;
+     VALUE Z;
+     VALUE A, B, C, D, E, F;
+     VALUE DX, DY, OME;
+     VALUE Ignore_non_eliptic;
+{
+    double *z, *ap, *bp, *cp, *dp, *ep, *fp;
+    double a, b, c, d, e, f, g, h, sum=0;
+    double dx, dy, ome;
+    struct NARRAY *na;
+    na_shape_t nx, ny, i, j;
+    VALUE res;
+
+    /* check & read arguments */
+    
+    if (NA_TYPE(Z) != NA_DFLOAT) rb_raise(rb_eArgError, "Z nust be DFLOAT");
+    if (NA_TYPE(A) != NA_DFLOAT) rb_raise(rb_eArgError, "A nust be DFLOAT");
+    if (NA_TYPE(B) != NA_DFLOAT) rb_raise(rb_eArgError, "B nust be DFLOAT");
+    if (NA_TYPE(C) != NA_DFLOAT) rb_raise(rb_eArgError, "C nust be DFLOAT");
+    if (NA_TYPE(D) != NA_DFLOAT) rb_raise(rb_eArgError, "D nust be DFLOAT");
+    if (NA_TYPE(E) != NA_DFLOAT) rb_raise(rb_eArgError, "E nust be DFLOAT");
+    if (NA_TYPE(F) != NA_DFLOAT) rb_raise(rb_eArgError, "F nust be DFLOAT");
+
+    if (NA_RANK(Z) != 2) rb_raise(rb_eArgError, "Z must be 2-dimensional");
+    nx = NA_SHAPE0(Z);
+    ny = NA_SHAPE1(Z);
+    if (NA_SHAPE0(A)!=nx || NA_SHAPE1(A)!=ny) rb_raise(rb_eArgError,
+                                                       "A: invalid shape");
+    if (NA_SHAPE0(B)!=nx || NA_SHAPE1(B)!=ny) rb_raise(rb_eArgError,
+                                                       "B: invalid shape");
+    if (NA_SHAPE0(C)!=nx || NA_SHAPE1(C)!=ny) rb_raise(rb_eArgError,
+                                                       "C: invalid shape");
+    if (NA_SHAPE0(D)!=nx || NA_SHAPE1(D)!=ny) rb_raise(rb_eArgError,
+                                                       "D: invalid shape");
+    if (NA_SHAPE0(E)!=nx || NA_SHAPE1(E)!=ny) rb_raise(rb_eArgError,
+                                                       "E: invalid shape");
+    if (NA_SHAPE0(F)!=nx || NA_SHAPE1(F)!=ny) rb_raise(rb_eArgError,
+                                                       "F: invalid shape");
+
+    GetNArray(Z, na); z = (double *)NA_PTR(na, 0);
+    GetNArray(A, na); ap = (double *)NA_PTR(na, 0);
+    GetNArray(B, na); bp = (double *)NA_PTR(na, 0);
+    GetNArray(C, na); cp = (double *)NA_PTR(na, 0);
+    GetNArray(D, na); dp = (double *)NA_PTR(na, 0);
+    GetNArray(E, na); ep = (double *)NA_PTR(na, 0);
+    GetNArray(F, na); fp = (double *)NA_PTR(na, 0);
+
+    dx = NUM2DBL(DX);
+    dy = NUM2DBL(DY);
+    if (dx==0.0) rb_raise(rb_eArgError, "dx == 0");
+    if (dy==0.0) rb_raise(rb_eArgError, "dy == 0");
+    ome = NUM2DBL(OME);
+
+    /* solve (1 step) */
+    for (j=1; j<ny-1; j++){
+        for (i=1; i<nx-1; i++){
+            a = ap[ID(i,j)] / (dx*dx);
+            b = bp[ID(i,j)] / (dx*dy);
+            c = cp[ID(i,j)] / (dy*dy);
+            if (Ignore_non_eliptic == Qfalse || Ignore_non_eliptic == Qnil ) {
+                if((a*c-b*b)<=0.0) 
+                    rb_raise(rb_eStandardError,"non-eliptic@[%d,%d]",i,j);
+            }
+            d = dp[ID(i,j)] / dx;
+            e = ep[ID(i,j)] / dy;
+            f = fp[ID(i,j)];
+            h = 2*(a+c);
+            g = ome * ( a*( z[ID(i-1,j)]+z[ID(i+1,j)] )
+                      + b/2*( z[ID(i+1,j+1)] - z[ID(i-1,j+1)] - z[ID(i+1,j-1)]
+                             +z[ID(i-1,j-1)] )
+                      + c*( z[ID(i,j-1)]+z[ID(i,j+1)] )
+                      + d/2*( z[ID(i+1,j)]-z[ID(i-1,j)] )
+                      + e/2*( z[ID(i,j+1)]-z[ID(i,j-1)] )
+                      - f - h*z[ID(i,j)]);
+            sum += g*g;
+            z[ID(i,j)] += g/h;
+        }
+    }
+    res = DBL2NUM( sqrt(sum) );
+    return(res);
+}
+
+void
+init_ganalysis_pde_ext()
+{
+    static VALUE mNumRu, mGA, mPDE;
+    mNumRu = rb_define_module("NumRu");
+    mGA = rb_define_module_under(mNumRu, "GAnalysis");
+    mPDE = rb_define_module_under(mGA, "PDE");
+    rb_define_module_function(mPDE, "SOR_2D_2ndorder_1step", 
+                              SOR_2D_2ndorder_1step, 11);
+}

data/gphys.gemspec

@@ -25,6 +25,7 @@ Gem::Specification.new do |spec|
   spec.require_paths = ["ext","lib"]
   spec.test_files    = spec.files.grep(%r{^(test|test_old|sample|testdata)/})
   spec.extensions << "ext/numru/gphys/extconf.rb"
+  spec.extensions << "ext/numru/ganalysis/extconf.rb"
 
   spec.post_install_message = "Thanks for installing! You can add extra libraries (i.e., ruby-lapack, rb-gsl) to enjoy powerful calculating and handling datasets."
 

data/lib/numru/ganalysis/eof.rb

@@ -92,7 +92,7 @@ module NumRu
         end
         w /= w.mean
         w.reshape!(n)
-      else
+      elsif new_grid.rank >= 2
         nc0 = new_grid.coord(0)
         nc1 = new_grid.coord(1)
         if !(opts[:disable_weight]||opts["disable_weight"]) &&
@@ -107,6 +107,8 @@ module NumRu
         else
           w = nil
         end
+      else
+        w = nil
       end
 
       ary = NArrayMiss.new(gphys.typecode, n_lost, n)

data/lib/numru/ganalysis/fitting.rb

@@ -215,14 +215,16 @@ module NumRu
       #   number of functions (also unsolvable).
       # 
       def least_square_fit(data, grid_locs, functions, ensemble_dims=nil,
-                           indep_dims=nil)
+                           indep_dims=nil, with_offset=true)
 
         #< argument check >
 
         grid_locs.each_with_index{|x,i| self.ensure_1D_NArray(x, i)}
         functions.each{|f| raise("Found non-Proc arg") if !f.is_a?(Proc)}
 
-        functions = functions + [@@unity]   # constanf offset
+        if with_offset
+          functions = functions + [@@unity]   # constanf offset
+        end
 
         ng = grid_locs.length
         rank = data.rank
@@ -336,9 +338,16 @@ module NumRu
           c = na
 
           # best fit
-          bf = c[-1]    # the constant offset
-          for i in 0...ms-1
-            bf += c[i]*fv[i]
+          if with_offset
+            bf = c[-1]    # the constant offset
+            for i in 0...ms-1
+              bf += c[i]*fv[i]
+            end
+          else
+            bf = 0.0
+            for i in 0...ms
+              bf += c[i]*fv[i]
+            end
           end
 
         else    # fitting multiple times
@@ -381,9 +390,16 @@ module NumRu
             end
           end
           cs = c.reshape(ms, *idshp_full)
-          bf = cs[-1,false]
-          for i in 0...ms-1
-            bf += cs[i,false]*fv[i]
+          if with_offset
+            bf = cs[-1,false]
+            for i in 0...ms-1
+              bf += cs[i,false]*fv[i]
+            end
+          else
+            bf = cs[-1,false] * 0
+            for i in 0...ms
+              bf += cs[i,false]*fv[i]
+            end
           end
 
         end

data/lib/numru/ganalysis/narray_ext.rb

@@ -0,0 +1,13 @@
+require "narray"
+require "numru/ganalysis/ganalysis_ext"
+
+class NArray
+  def cum_sum(dim)
+    case self.typecode
+    when DFLOAT
+      NumRu::NArrayExt.cum_sum_dfloat(self,dim)
+    else
+      raise "Sorry, this narray type #{self.typecode} is not supported."
+    end
+  end
+end

data/lib/numru/ganalysis/pde.rb

@@ -0,0 +1,90 @@
+require "numru/gphys"
+require "numru/ganalysis/ganalysis_ext"
+
+module NumRu
+  module GAnalysis
+    module PDE
+      module_function
+      #
+      # = Solve 2-dim 2nd order PDE by the succesive over-relaxation method
+      # 
+      # ARGUMENTS.
+      # * z [in-out, 2D dfloat NArray] : When in, initial values. When out,
+      #   the result. Boundary values are not changed (Dirichlet problem)
+      #   (developper's memo: Neuman cond can be supported as an option)
+      # * a, b, c, d, e, f [in, 2D dfloat NArray with the same shape as z] :
+      #   Specifies the PDF as
+      #      a z_xx + 2*b z_xy + c z_yy + d z_x + e z_y = f
+      #               ^^^
+      #   Please note that 2*b is the coefficient of z_xy.
+      #   x is the first (0th) NArray dimension.
+      # * dx, dy [Float] : grid spacings
+      # * ome [Float] : the over-relaxation parameter 1<=ome<2.
+      #   For a large-scale poisson equation, should be ~ 2 (e.g. 1.9).
+      # * eps [optional, Float] : conversion threshold (e.g. 1e-5).
+      #   Compared with |increment|/|F| (| | is the L2 norm).
+      #   When |f| == 0 (homogenous), compared simply with |increment|.
+      # * maxi [optional, Integer]: max iteration times(default, 5*[nx,ny].max).
+      #   Since SOR (or the Gauss-Seidel method) acts like a stepwise diffusion,
+      #   it must be greater than the along-x and along-y grid sizes.
+      # * ignore_non_eliptic : if true (non-nil,non-false), do not raise
+      #   error when the coeeficients are not entirely eliptic.
+      # 
+      # RETURN VALUE
+      # * |last increment|/|F| of |last increment| (to be compared with eps)
+      # 
+      def SOR_2D_2ndorder(z, a, b, c, d, e, f, dx, dy, ome, eps: nil, maxi: nil,
+                          ignore_non_eliptic: false)
+        lf = Math.sqrt( (f**2).sum )  # L2 norm of f
+        lf = 1.0 if lf==0   # when |f|==0 (homogeneous), no-division by |f|.
+        res = nil
+        if !maxi
+          maxi = [ z.shape[0], z.shape[1] ].max * 5  # default max itr times
+        end
+        convd = false
+        for i in 0...maxi
+          res = SOR_2D_2ndorder_1step(z, a, b, c, d, e, f, dx, dy, ome,
+                                      ignore_non_eliptic)
+          #p res/lf, z
+          if (eps && res/lf < eps)
+            convd = true
+            break
+          end
+        end
+        if (eps && !convd)
+          raise("Max iteration times (#{maxi}) reached before convergence" +
+                " (#{res/lf} > #{eps}). Change ome (#{ome}) or specify maxi.")
+        end
+        #p i,res/lf #, z
+        res/lf
+      end
+    end
+  end
+end
+
+################################################
+##### test part ######
+if $0 == __FILE__
+  require "numru/ggraph"
+  include NumRu
+
+  #nx = ny = 9
+  nx = ny = 91
+  z = NArray.float(nx,ny)
+  a = c = NArray.float(nx,ny).fill!(1.0)
+  b = d = e = NArray.float(nx,ny)
+  f = NArray.float(nx,ny)
+  f[nx/2,ny/2] = 1.0
+  dx = dy = 1.0
+  #ome = 1.9
+  #GAnalysis::PDE.SOR_2D_2ndorder(z, a, b, c, d, e, f, dx, dy, ome)
+=begin
+  (1.0..1.91).step(0.1){|ome|
+    puts "ome = #{ome}"
+    GAnalysis::PDE.SOR_2D_2ndorder(z, a, b, c, d, e, f, dx, dy, ome)
+  }
+=end
+  eps = 1e-6
+  ome = 1.95
+  GAnalysis::PDE.SOR_2D_2ndorder(z, a, b, c, d, e, f, dx, dy, ome, eps: eps)
+end

data/lib/numru/ggraph.rb

@@ -2839,11 +2839,7 @@ module NumRu
 
       @@used_fullcolor_tone = false
       val = gp.data.val
-      if ( opts['ltone'] && 
-          ( opts['tonf'] || opts['auto'] && !opts['tonb'] && !opts['tonc'] &&
-            ( val.length >= TONE_TONF_THRES_SIZE || val.shape.min >= TONE_TONF_THRES_LEN ) ) )
-        DCL.uetonf(val)
-      elsif opts['fullcolor']
+      if opts['fullcolor']
         @@used_fullcolor_tone = true
         sopt = opts.dup.delete_if{|k,v| !DCLExt.shade_1_option_keys.include?(k)}
         DCLExt.ui_shade_1(val, sopt)
@@ -2851,6 +2847,11 @@ module NumRu
         DCL.uetonb(val)
       elsif opts['tonc'] && opts['ltone']
         DCL.uetonc(val)
+      elsif ( opts['ltone'] && 
+              ( opts['tonf'] ||
+                opts['auto']  && ( val.length >= TONE_TONF_THRES_SIZE ||
+                                   val.shape.min >= TONE_TONF_THRES_LEN ) ) )
+        DCL.uetonf(val)
       else
         DCL.uetone(val)
       end

data/lib/numru/gphys.rb

@@ -12,4 +12,5 @@ require 'numru/gphys_ext'  # extension library
 require 'numru/gphys/interpolate'
 require 'numru/gphys/gphys_dim_op'
 require 'numru/gdir'
+require 'numru/gphys/derivative'
 # require 'numru/gphys/ep_flux' # Made optional. Require it explicitly if needed

data/lib/numru/gphys/gphys.rb

@@ -1210,7 +1210,8 @@ module NumRu
         grid = Grid.new(*axes)
         if gp0.assoc_coords
           assoc_coords = gp0.assoccoordnames.collect do |aname|
-            GPhys.join( gpnary.collect{|gp| gp.assoc_coord_gphys(aname)}, true )
+            GPhys.join( gpnary.collect{|gp| gp.assoc_coord_gphys(aname)}, true,
+                        true )
           end
           grid.set_assoc_coords(assoc_coords)
         end
@@ -1222,7 +1223,7 @@ module NumRu
         GPhys.new(grid, data)
       end
 
-      def GPhys.join_md(gpnary)
+      def GPhys.join_md(gpnary, no_sort=false)
         #< Check >
 
         if !gpnary.is_a?(NArray)
@@ -1283,7 +1284,7 @@ module NumRu
         end
 
         #< Sort along dimensions to join >
-        gpnary = __sort_gpnary(gpnary)
+        gpnary = __sort_gpnary(gpnary) unless no_sort
 
         #< Join! >
         self.join_md_nocheck(gpnary)
@@ -1294,7 +1295,7 @@ module NumRu
       # ARGUMENT
       # * gpnarray [Array (or 1D NArray) of GPhys]
       # 
-      def GPhys.join(gpary, ignore_overlap=false)
+      def GPhys.join(gpary, ignore_overlap=false, no_sort=false)
 
         #< initialization with the first GPhys object >
 
@@ -1332,7 +1333,7 @@ module NumRu
         gpnary = gpstore.to_na
 
         #< Sort along dimensions to join >
-        gpnary = __sort_gpnary(gpnary)
+        gpnary = __sort_gpnary(gpnary) unless no_sort
 
         #< Join! >
         self.join_md_nocheck(gpnary)

data/lib/numru/gphys/version.rb

@@ -1,6 +1,6 @@
 module NumRu
   class GPhys
     # Add subsubminor version while under development; remove it and advance version to release
-    VERSION = "1.5.5"
+    VERSION = "1.5.6"
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gphys
 version: !ruby/object:Gem::Version
-  version: 1.5.5
+  version: 1.5.6
 platform: ruby
 authors:
 - Takeshi Horinouchi
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-03-20 00:00:00.000000000 Z
+date: 2019-03-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: narray
@@ -132,6 +132,7 @@ executables:
 - grads2nc_with_gphys
 extensions:
 - ext/numru/gphys/extconf.rb
+- ext/numru/ganalysis/extconf.rb
 extra_rdoc_files: []
 files:
 - ".ChangeLog.until201303"
@@ -539,6 +540,10 @@ files:
 - doc/update_rdoc
 - doc/varray.html
 - doc/varraycomposite.html
+- ext/numru/ganalysis/ext_init.c
+- ext/numru/ganalysis/extconf.rb
+- ext/numru/ganalysis/narray_ext_dfloat.c
+- ext/numru/ganalysis/pde_ext.c
 - ext/numru/gphys/dim_op.c
 - ext/numru/gphys/ext_coord.c
 - ext/numru/gphys/ext_init.c
@@ -559,6 +564,8 @@ files:
 - lib/numru/ganalysis/log_p.rb
 - lib/numru/ganalysis/met.rb
 - lib/numru/ganalysis/met_z.rb
+- lib/numru/ganalysis/narray_ext.rb
+- lib/numru/ganalysis/pde.rb
 - lib/numru/ganalysis/planet.rb
 - lib/numru/ganalysis/qg.rb
 - lib/numru/ganalysis/sigma_coord.rb